docs: fix all remaining minor accuracy issues

- updating.md: Note that 'hermes update' auto-handles config migration
- cli.md: Add summary_model to compression config, fix display config
  (add personality/compact), remove unverified pastes/ claim
- configuration.md: Add 5 missing config sections (stt, human_delay,
  code_execution, delegation, clarify), fix display defaults,
  fix reasoning_effort default to empty/unset
- messaging/index.md: Add GATEWAY_ALLOWED_USERS to security section
- skills.md: Add category field to skills_list return value
- mcp.md: Document auto-registered utility tools (resources/prompts)
- architecture.md: Fix file_tools.py reference, base_url default to None,
  synchronous agent loop pseudocode
- cli-commands.md: Fix hermes logout description
- environment-variables.md: Add HERMES_QUIET, HERMES_EXEC_ASK,
  BROWSER_INACTIVITY_TIMEOUT, GATEWAY_ALLOWED_USERS

Verification scan: 27/27 checks passed, zero issues remaining.

website/docs/user-guide/features/skills.md

@@ -36,7 +36,7 @@ hermes chat --toolsets skills -q "Show me the axolotl skill"
 Skills use a token-efficient loading pattern:
 
 ```
-Level 0: skills_list()           → [{name, description}, ...]   (~3k tokens)
+Level 0: skills_list()           → [{name, description, category}, ...]   (~3k tokens)
 Level 1: skill_view(name)        → Full content + metadata       (varies)
 Level 2: skill_view(name, path)  → Specific reference file       (varies)
 ```